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Fix casting of range filter start/end to float #11021

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Sep 27, 2024
Merged

Fix casting of range filter start/end to float #11021

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6 changes: 3 additions & 3 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -345,7 +345,7 @@
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include>,
${dataFilterValue.start}
cast(${dataFilterValue.start} as float)
)
) &lt; exp(-11)
</when>
Expand All @@ -354,13 +354,13 @@
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include> &gt; ${dataFilterValue.start}
</include> &gt; cast(${dataFilterValue.start} as float)
</if>
<if test="dataFilterValue.end != null">
AND
<include refid="castStringValueToFloat">
<property name="attribute_value" value="attribute_value"/>
</include> &lt;= ${dataFilterValue.end}
</include> &lt;= cast(${dataFilterValue.end} as float)
</if>
</otherwise>
</choose>
Expand Down
11 changes: 10 additions & 1 deletion test/api-e2e/specs/clinical-data-filters.json
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Original file line number Diff line number Diff line change
@@ -1,4 +1,12 @@
[
[
{
"name":"Range start comparison",
"note":"Range boundaries must be cast to floats in order to evaluate properly",
"studies":["cesc_tcga_pan_can_atlas_2018"],
"tests":[
{"hash":50301331,"filterString":"Fraction Genome Altered: < x ≤ 0.30.35","data":{"clinicalDataFilters":[{"attributeId":"FRACTION_GENOME_ALTERED","values":[{"end":0.35,"start":0.3}]}],"studyIds":["cesc_tcga_pan_can_atlas_2018"],"alterationFilter":{"copyNumberAlterationEventTypes":{"AMP":true,"HOMDEL":true},"mutationEventTypes":{"any":true},"structuralVariants":null,"includeDriver":true,"includeVUS":true,"includeUnknownOncogenicity":true,"includeUnknownTier":true,"includeGermline":true,"includeSomatic":true,"includeUnknownStatus":true,"tiersBooleanMap":{}}},"url":"/api/column-store/structuralvariant-genes/fetch?","label":"StructuralVariantGenes","studies":["cesc_tcga_pan_can_atlas_2018"],"filterUrl":"/study/summary?id=cesc_tcga_pan_can_atlas_2018#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"FRACTION_GENOME_ALTERED\",\"values\":[{\"end\":0.35,\"start\":0.3}]}],\"studyIds\":[\"cesc_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"}
]
},
{
"name": "Age at Which Sequencing was Reported <= 25",
"note": "Filter result should include patients/samples with special age value of '<18'",
Expand Down Expand Up @@ -3575,6 +3583,7 @@
],
"filterUrl": "/study/summary?id=brca_akt1_genie_2019%2Cbrca_tcga_pan_can_atlas_2018%2Cskcm_tcga_pan_can_atlas_2018#filterJson={\"clinicalDataFilters\":[{\"attributeId\":\"AGE\",\"values\":[{\"start\":45,\"end\":50},{\"start\":50,\"end\":55},{\"start\":55,\"end\":60},{\"start\":60,\"end\":65},{\"start\":65,\"end\":70}]},{\"attributeId\":\"MUTATION_COUNT\",\"values\":[{\"start\":20,\"end\":40},{\"start\":40,\"end\":60},{\"start\":60,\"end\":80}]},{\"attributeId\":\"ETHNICITY\",\"values\":[{\"value\":\"Hispanic Or Latino\"}]}],\"studyIds\":[\"brca_akt1_genie_2019\",\"brca_tcga_pan_can_atlas_2018\",\"skcm_tcga_pan_can_atlas_2018\"],\"alterationFilter\":{\"copyNumberAlterationEventTypes\":{\"AMP\":true,\"HOMDEL\":true},\"mutationEventTypes\":{\"any\":true},\"structuralVariants\":null,\"includeDriver\":true,\"includeVUS\":true,\"includeUnknownOncogenicity\":true,\"includeUnknownTier\":true,\"includeGermline\":true,\"includeSomatic\":true,\"includeUnknownStatus\":true,\"tiersBooleanMap\":{}}}"
}

]
}
]
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